Volume 136, Issue 21, 07 June 2012

We perform molecular dynamics simulations of supercritical water (SCW) with a wide range of densities along a near critical isotherm using the simple point charge extended (SPC/E) pair potential in order to study the entropy and the solvation shell structure around a central water molecule. It is shown that both the translational and orientational twoparticle correlationentropy terms can serve as the metrics of the translationalorientational structural orders in water and it is revealed that the translational structural order is very sensitive to the density variation in the gaslike and liquidlike region, while the orientational structural order is much more dependent upon compression in the mediumdensity SCW region. The comparison of the magnitudes of the full thermodynamic excess entropy and twoparticle correlationentropy confirms the recent findings that the manybody terms other than twobody ones also present significant and nonneglectable contributions to the full excess entropy for the highly anomalous fluids like water. The analysis of entropy terms as a function of intermolecular distance and the orientational distribution functions as well as the threedimensional spatialdistribution functions indicate that the structural order occurs only in a much more diffused first solvation shell due to the elongated hydrogen bonds under supercritical conditions. It is revealed that no obvious second or higher neighbor shells occur in SCW, in contrast with the feature of normal liquid water that the anomalous decrease of translational order upon compression occurs mainly in the second shell.
 PERSPECTIVES


Perspective: Quantum or classical coherence?
View Description Hide DescriptionSome coherenceeffects in chemical dynamics are described correctly by classical mechanics, while others only appear in a quantum treatment—and when these are observed experimentally it is not always immediately obvious whether their origin is classical or quantum. Semiclassical theory provides a systematic way of adding quantum coherence to classical molecular dynamics and thus provides a useful way to distinguish between classical and quantum coherence. Several examples are discussed which illustrate both cases. Particularly interesting is the situation with electronically nonadiabatic processes, where sometimes whether the coherenceeffects are classical or quantum depends on what specific aspects of the process are observed.
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 COMMUNICATIONS


Communication: Fast and local predictors of the violation of the StokesEinstein law in polymers and supercooled liquids
View Description Hide DescriptionThe violation of the StokesEinstein (SE) law is investigated in a melt of linear chains by extensive moleculardynamics simulations. It is found that the SE breakdown is signaled (with 5% uncertainty) by the monomer meansquare displacement ⟨u ^{2}⟩ on the picosecond time scale. On this time scale the displacements of the nextnextnearest neighbors are uncorrelated. It is shown that: (i) the SE breakdown occurs when ⟨u ^{2}⟩ is smaller than the breadth of the distribution of the square displacements to escape from the firstneighbors cage, (ii) the dynamical heterogeneity affects the form of the master curve of the universal scaling between the structural relaxation and ⟨u ^{2}⟩.

Communication: Clusters of absorbing disks on a reflecting wall: Competition for diffusing particles
View Description Hide DescriptionTrapping of diffusing particles by a cluster of absorbing disks on the otherwise reflecting wall is a manifestly manybody problem because of the disk competition for the particles. By replacing the cluster with an effective uniformly absorbing spot, we derive a simple formula for the rate constant that characterizes the trapping. The formula shows how the rate constant depends on the size and shape of the cluster.

Communication: The structures of small cationic gasphase platinum clusters
View Description Hide DescriptionThe structures of small platinumclusters are determined using farinfrared multiple photondissociation spectroscopy of their argon complexes combined with density functional theory calculations. The clusters are found to have compact structures, and and already favor threedimensional geometries, in contrast to a number of earlier predictions. Challenges in applying density functional theory to 3rd row transition metal clusters are addressed. Preliminary calculations suggest that the effects of spinorbit coupling do not change the favoured lowestenergy isomers.

Communication: Phase incremented echo train acquisition in NMR spectroscopy
View Description Hide DescriptionWe present an improved and general approach for implementing echo train acquisition (ETA) in magnetic resonancespectroscopy, particularly where the conventional approach of CarrPurcellMeiboomGill (CPMG) acquisition would produce numerous artifacts. Generally, adding ETA to any Ndimensional experiment creates an N + 1 dimensional experiment, with an additional dimension associated with the echo count, n, or an evolution time that is an integer multiple of the spacing between echo maxima. Here we present a modified approach, called phase incremented echo train acquisition (PIETA), where the phase of the mixing pulse and every other refocusing pulse, ϕ_{ P }, is incremented as a single variable, creating an additional phase dimension in what becomes an N + 2 dimensional experiment. A Fourier transform with respect to the PIETA phase, ϕ_{ P }, converts the ϕ_{ P } dimension into a Δp dimension where desired signals can be easily separated from undesired coherence transfer pathway signals, thereby avoiding cumbersome or intractable phase cycling schemes where the receiver phase must follow a master equation. This simple modification eliminates numerous artifacts present in NMR experiments employing CPMG acquisition and allows “singlescan” measurements of transverse relaxation and Jcouplings. Additionally, unlike CPMG, we show how PIETA can be appended to experiments with phase modulated signals after the mixing pulse.
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 ARTICLES

 Theoretical Methods and Algorithms

Juxtaposing density matrix and classical pathbased wave packet dynamics
View Description Hide DescriptionIn many physical, chemical, and biological systems energy and charge transfer processes are of utmost importance. To determine the influence of the environment on these transport processes, equilibrium molecular dynamics simulations become more and more popular. From these simulations, one usually determines the thermal fluctuations of certain energy gaps, which are then either used to perform ensembleaveraged wave packet simulations, also called Ehrenfest dynamics, or to employ a density matrix approach via spectral densities. These two approaches are analyzed through energy gap fluctuations that are generated to correspond to a predetermined spectral density. Subsequently, density matrix and wave packet simulations are compared through population dynamics and absorption spectra for different parameter regimes. Furthermore, a previously proposed approach to enforce the correct longtime behavior in the wave packet simulations is probed and an improvement is proposed.

Predicting patchy particle crystals: Variable box shape simulations and evolutionary algorithms
View Description Hide DescriptionWe consider several patchy particle models that have been proposed in literature and we investigate their candidate crystal structures in a systematic way. We compare two different algorithms for predicting crystal structures: (i) an approach based on Monte Carlo simulations in the isobaricisothermal ensemble and (ii) an optimization technique based on ideas of evolutionary algorithms. We show that the two methods are equally successful and provide consistent results on crystalline phases of patchy particle systems.

A discrete interaction model/quantum mechanical method for simulating surfaceenhanced Raman spectroscopy
View Description Hide DescriptionWe have derived and implemented analytical gradients for the discrete interaction model/quantum mechanics (DIM/QM) method. DIM/QM combines an atomistic electrodynamics model with timedependent density functional theory and thus enables modeling of the optical properties for a molecule while taking into account the local environment of a nanoparticle's surface. The DIM/QM analytical gradients allow for geometry optimizations, vibrational frequencies, and Raman spectra to be simulated for molecules interacting with metal nanoparticles. We have simulated the surfaceenhanced Raman scattering(SERS)spectra for pyridine adsorbed on different sites of icosahedral nanoparticles with diameters between 1 and 8 nm. To describe the adsorption of the pyridine molecule onto the metal surface, we have implemented a coordinationdependent force field to differentiate the various local surface environments. We find that the DIM/QM method predicts geometries and frequencies that are in good agreement with full QM simulations and experiments. For the simulated SERSspectra of pyridine, we find a significant dependence on the adsorption site and the size of the metal nanoparticle. This illustrates the importance of accounting for the local environment around the molecule. The Raman enhancement factors are shown to roughly mirror the magnitude of the nanoparticle's local field about the molecule. Because the simulated nanoparticles are small, the plasmon peaks are quite broad which results in weak local electric fields and thus modest Raman enhancement factors.

A divide and conquer realspace approach for allelectron molecular electrostatic potentials and interaction energies
View Description Hide DescriptionA computational scheme to perform accurate numerical calculations of electrostatic potentials and interaction energies for molecular systems has been developed and implemented. Molecular electron and energy densities are divided into overlapping atomcentered atomic contributions and a threedimensional molecular remainder. The steep nuclear cusps are included in the atomcentered functions making the threedimensional remainder smooth enough to be accurately represented with a tractable amount of grid points. The onedimensional radial functions of the atomcentered contributions as well as the threedimensional remainder are expanded using finite element functions. The electrostatic potential is calculated by integrating the Coulomb potential for each separate density contribution, using our tensorial finite element method for the threedimensional remainder. We also provide algorithms to compute accurate electronelectron and electronnuclear interactions numerically using the proposed partitioning. The methods have been tested on allelectron densities of 18 reasonable large molecules containing elements up to Zn. The accuracy of the calculated Coulomb interaction energies is in the range of 10^{−3} to 10^{−6} E _{h} when using an equidistant grid with a step length of 0.05 a _{0}.

Accurate relativistic energyconsistent pseudopotentials for the superheavy elements 111 to 118 including quantum electrodynamic effects
View Description Hide DescriptionEnergyconsistent twocomponent semilocal pseudopotentials for the superheavy elements with atomic numbers 111–118 have been adjusted to fully relativistic multiconfiguration Dirac–Hartree–Fock calculations based on the Dirac–Coulomb Hamiltonian, including perturbative corrections for the frequencydependent Breit interaction in the Coulomb gauge and lowestorder quantum electrodynamic effects. The pseudopotential core includes 92 electrons corresponding to the configuration [Xe]4f ^{14}5d ^{10}5f ^{14}. The parameters for the elements 111–118 were fitted by twocomponent multiconfiguration Hartree–Fock calculations in the intermediate coupling scheme to the total energies of 267 up to 797 J levels arising from 31 up to 62 nonrelativistic configurations, including also anionic and highly ionized states, with mean absolute errors clearly below 0.02 eV for averages corresponding to nonrelativistic configurations. Primitive basis sets for one and twocomponent pseudopotential calculations have been optimized for the ground and excited states and exhibit finite basis set errors with respect to the finitedifference Hartree–Fock limit below 0.01 and 0.02 eV, respectively. General contraction schemes have been applied to obtain valence basis sets of polarized valence double to quadruplezeta quality. Results of atomic test calculations in the intermediate coupling scheme at the Fockspace coupledcluster level are in good agreement with those of corresponding fully relativistic allelectron calculations based on the Dirac–Coulomb–Breit Hamiltonian. The results demonstrate besides the wellknown need of a relativistic treatment at the Dirac–Coulomb level also the necessity to include higherorder corrections for the superheavy elements.

[N]pT Monte Carlo simulations of the clustercrystalforming penetrable sphere model
View Description Hide DescriptionCertain models with purely repulsive pair interactions can form cluster crystals with multiplyoccupied lattice sites. Simulating these models’ equilibrium properties is, however, quite challenging. Here, we develop an expanded isothermalisobaric [N]pT ensemble that surmounts this problem by allowing both particle number and lattice spacing to fluctuate. It is particularly efficient at high T, where particle insertion is facile. Using this expanded ensemble and thermodynamic integration, we solve the phase diagram of a prototypical clustercrystal former, the penetrable sphere model, and compare the results with earlier theoretical predictions. At high temperatures and densities, the equilibrium occupancy of facecentered cubic crystal increases linearly. At low temperatures, although plateaus at integer values, the crystal behavior changes continuously with density. The previously ambiguous crossover around T ∼ 0.1 is resolved.

Multidimensional wavepacket and potential reconstruction by resonant coherent antiStokes Raman scattering: Application to H_{2}O and HOD
View Description Hide DescriptionWe have recently proposed a methodology for reconstructingexcitedstate (ExS) molecular wavepackets, and the corresponding potential energy surface, from threepulse resonant coherent antiStokes Raman scattering and knowledge of the groundstate potential [Avisar and Tannor, Phys. Rev. Lett.106, 170405 (2011)10.1103/PhysRevLett.106.170405]. The methodology is general for polyatomics and applies to any form of ExS potential – bound or dissociative. In our previous work we demonstrated the method on diatomics. Here, we demonstrate the method on the triatomics H_{2}O and HOD, reconstructing the ExS wavepacket and potential in the two bondstretching coordinates.

Replica theory of the rigidity of structural glasses
View Description Hide DescriptionWe present a first principle scheme to compute the rigidity, i.e., the shearmodulus of structural glasses at finite temperatures using the cloned liquid theory, which combines the replica theory and the liquid theory. With the aid of the replica method which enables disentanglement of thermal fluctuations in liquids into intrastate and interstate fluctuations, we extract the rigidity of metastable amorphous solid states in the supercooled liquid and glass phases. The result can be understood intuitively without replicas. As a test case, we apply the scheme to the supercooled and glassy state of a binary mixture of softspheres. The result compares well with the shearmodulus obtained by a previous molecular dynamic simulation. The rigidity of metastable states is significantly reduced with respect to the instantaneous rigidity, namely, the Born term, due to nonaffine responses caused by displacements of particles inside cages at all temperatures down to T = 0. It becomes nearly independent of temperature below the Kauzmann temperature T _{K}. At higher temperatures in the supercooled liquid state, the nonaffine correction to the rigidity becomes stronger suggesting melting of the metastable solid state. Interstate part of the static response implies jerky, intermittent stressstrain curves with static analogue of yielding at mesoscopic scales.

Maximumentropy closure of hydrodynamic moment hierarchies including correlations
View Description Hide DescriptionGeneralized hydrodynamic moment hierarchies are derived which explicitly include nonequilibrium twoparticle and higherorder correlations. The approach is adapted to strongly correlated media and nonequilibrium processes on short time scales which necessitate an explicit treatment of timeevolving correlations. Closure conditions for the extended moment hierarchies are formulated by a maximumentropy approach, generalizing related closure procedures for kinetic equations. A selfconsistent set of nonperturbative dynamical equations are thus obtained for a chosen set of singleparticle and twoparticle (and possibly higherorder) moments. Analytical results are derived for generalized Gaussian closures including the dynamic pair distribution function and a twoparticle correction to the current density. The maximumentropy closure conditions are found to involve the Kirkwood superposition approximation.

Forcedependent mobility and entropic rectification in tubes of periodically varying geometry
View Description Hide DescriptionWe investigate transport of point Brownian particles in a tube formed by identical periodic compartments of varying diameter, focusing on the effects due to the compartment asymmetry. The paper contains two parts. First, we study the forcedependent mobility of the particle. The mobility is a symmetric nonmonotonic function of the driving force, F, when the compartment is symmetric. Compartment asymmetry gives rise to an asymmetric forcedependent mobility, which remains nonmonotonic when the compartment asymmetry is not too high. The Fdependence of the mobility becomes monotonic in tubes formed by highly asymmetric compartments. The transition of the Fdependence of the mobility from nonmonotonic to monotonic behavior results in important consequences for the particle motion under the action of a timeperiodic force with zero mean, which are discussed in the second part of the paper: In a tube formed by moderately asymmetric compartments, the particle under the action of such a force moves with an effective drift velocity that vanishes at small and large values of the force amplitude having a maximum in between. In a tube formed by highly asymmetric compartments, the effective drift velocity monotonically increases with the amplitude of the driving force and becomes unboundedly large as the amplitude tends to infinity.

Quantum charge transport and conformational dynamics of macromolecules
View Description Hide DescriptionWe study the dynamics of quantum excitations inside macromolecules which can undergo conformational transitions. In the first part of the paper, we use the path integral formalism to rigorously derive a set of coupled equations of motion which simultaneously describe the molecular and quantum transportdynamics, and obey the fluctuation/dissipation relationship. We also introduce an algorithm which yields the most probable molecular and quantum transport pathways in rare, thermally activated reactions. In the second part of the paper, we apply this formalism to simulate the propagation of a quantum charge during the collapse of a polymer from an initial stretched conformation to a final globular state. We find that the charge dynamics is quenched when the chain reaches a molten globule state. Using random matrix theory we show that this transition is due to an increase of quantum localization driven by dynamical disorder. We argue that collapsing conducting polymers may represent a physical realization of quantum smallworld networks with dynamical rewiring probability.

Chainlength and modedelocalization dependent amideI anharmonicity in peptide oligomers
View Description Hide DescriptionThe diagonal anharmonicities of the amideI mode in the alanine oligomers are examined in the normalmode basis by ab initio calculations. The selected oligomers range from dimer to heptamer, in either the αhelical or βsheet conformations. It is found that the anharmonicity varies from mode to mode within the same oligomer. For a given amideI mode, the anharmonicity is closely related to the delocalization extent of the mode: the less it delocalizes, the larger the anharmonicity it has. Thus, the singlemode potential energy distribution (PED_{max}) can be used as an indicator of the magnitude of the anharmonicity. It is found that as the peptide chain length increases, the averaged diagonal anharmonicity generally decreases; however, the sum of the averaged diagonal and offdiagonal anharmonicities within a peptide roughly remains a constant for all the oligomers examined, indicating the excitonic characteristics of the amideI modes. Excitonic coupling tends to decrease the diagonal anharmonicities in a coupled system with multiple chromophores, which explains the observed behavior of the anharmonicities. The excitonic nature of the amideI band in peptide oligomers is thus verified by the anharmonic computations. Isotopic substitution effect on the anharmonicities and mode localizations of the amideI modes in peptides is also discussed.
 Advanced Experimental Techniques

Production of a beam of highly vibrationally excited CO using perturbations
View Description Hide DescriptionAn intense molecular beam of CO (X ^{1}Σ^{+}) in high vibrational states (v = 17, 18) was produced by a new approach that we call PUMP – PUMP – PERTURB and DUMP. The basic idea is to access high vibrational states of CO e ^{3}Σ^{−} via a twophoton doubly resonant transition that is perturbed by the A ^{1}Π state. DUMP ing from this mixed (predominantly triplet) state allows access to high vibrational levels of CO (X ^{1}Σ^{+}). The success of the approach, which avoids the use of vacuum UV radiation in any of the excitation steps, is proven by laser induced fluorescence and resonance enhanced multiphoton ionization spectroscopy.
 Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Fragmentation cross sections of protonated water clusters
View Description Hide DescriptionWe have measured fragmentation cross sections of protonated water cluster cations (H_{2}O)_{ n=30−50}H^{+} by collision with water molecules. The clusters have welldefined sizes and internal energies. The collisionenergy has been varied from 0.5 to 300 eV. We also performed the same measurements on deuterated water clusters (D_{2}O)_{ n=5−45}D^{+} colliding with deuterated water molecules. The main fragmentation channel is shown to be a sequential thermal evaporation of single molecules following an initial transfer of relative kinetic energy into internal energy of the cluster. Unexpectedly, that initial transfer is very low on average, of the order of 1% of collisionenergy. We evaluate that for direct collisions (i.e., within the hard sphere radius), the probability for observing no fragmentation at all is more than 35%, independently of cluster size and collisionenergy, over our range of study. Such an effect is well known at higher energies, where it is attributed to electronic effects, but has been reported only in a theoretical study of the collision of helium atoms with sodiumclusters in that energy range, where only vibrational excitation occurs.

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm^{−1} studied by Fourier transform infrared spectroscopy and stateoftheart ab initio calculations
View Description Hide DescriptionDifluoromethane (CH2F2, HFC32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibrationrotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and rovibrational properties of CH2F2, providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to highlevel electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm^{−1}. Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and rovibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm^{−1} while intensities are predicted within few km mol^{−1} from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the ν1⟩, 2ν8⟩, 2ν2⟩ three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and rovibrational mixings over the whole 400–5000 cm^{−1} region is also demonstrated by spectacular spectral simulations carried out by using the rovibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH2F2 as a prototype molecule to test ab initio calculations and theoretical models.